|
| Status |
Public on Jan 31, 2023 |
| Title |
D114Eb_2_min_log_RNAPChIP [R142b_2_min_log] |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organism |
Escherichia coli |
| Characteristics |
strain: D114E lrp at thyA
lineage: B
biological replicate: 2
media: Min
growth_phase: Log
chip antibody: RNAP
|
| Growth protocol |
Cells were grown in M9 Minimal media (Min) or the same media supplemented with 0.2% each of L-leucine, L-isoleucine, and L-valine (LIV) at 37 degrees Celcius until OD600 = 0.2 (log-phase) or 12 hours after log-phase (stat phase) and crosslinked with 1% formaldehyde
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell pellets were lysed and sonicated. Input samples were set aside and the remainder of each lysate was split in half where the Lrp-DNA complexes and RNAP-DNA complexes were isolated with their respective antibodies; Neoclone W0023 (the RNA polymerase antibody), lot # 2019G15-002, Lrp antibody is NeoClone custom antibody clone# 1G4D9A10, Lot# 2016E25-001.
ChIP-seq libraries were prepared for sequencing with the NEBNext UltraII DNA kit using an OpenTrons2 robot
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
processed data file:
142b_min_log_rnap_LrpKOsub.bedgraph
D114E_min_log_deseq.csv
|
| Data processing |
Adapter trimming: cutadapt 3.4
Quality trimming: TrimmomaticPE 0.39 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10
Alignment: bowtie2 v2.2.5 (arguments: --end-to-end –very-sensitive -I 0 -X 2000)
For Lrp ChIP samples – Occupancy quantitation (IPOD-HR pipeline v2.3.6)
For RNA polymerase ChIP samples – read counting with GenomicAlignments 1.26.0 (running under R 4.0.5)
For RNA polymerase ChIP samples – differential expression calling with deseq2 1.30.1 (running under R 4.0.5)
Genome_build: E. coli MG1655 (U00096.3)
Supplementary_files_format_and_content: bedgraph files of normalized occupancy (after subtraction of delta lrp signal)
Supplementary_files_format_and_content: csv files containing Deseq results
|
| |
|
| Submission date |
Mar 07, 2022 |
| Last update date |
Jan 31, 2023 |
| Contact name |
Lydia Freddolino |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Michigan
|
| Department |
Biological Chemistry
|
| Lab |
Freddolino Lab
|
| Street address |
1150 W. Medical Center Dr., MSRB 3 room 3315
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109-0600 |
| Country |
USA |
| |
|
| Platform ID |
GPL25368 |
| Series (1) |
| GSE198120 |
High throughput analysis of binding of E. coli Lrp mutants |
|
| Relations |
| BioSample |
SAMN26514493 |
| SRA |
SRX14407057 |
